[Bioperl-l] how to get positive and frame in blastx use searchio?

[Jason Stajich]

Get a HSP (see the Docs if it isn't clear)
For BLASTX
$hsp->query->frame will give you the frame
For TBLASTN
$hsp->hit->frame will give you the frame
For TBLASTX
you can get the query and hit frame by calling both of those methods.

$hsp->frac_conserved('hit') will give you the fraction of the hit which is
'positive'  $hsp->frac_conserved('query') is the fraction of the query and
$hsp->frac_conserved('total') will give you the overall positive fraction
- multiply this by the hsp length ($hsp->length('total')) to get the
number of positive bases.

You can also get the specific residues which are conserver or identical
with the seq_inds() method.

-jason


On Thu, 17 Apr 2003, Magic Fang wrote:

> it seem that searchio handle all blast program result, but if it ignores
> this two values? oh, frame value without directory info.
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu